Those Rusty coils are the softest 4.5's I know of for XJ's (too soft for me), with the RS9000's, you
should be able to adjust in a nice, super plush ride.
The problem is, at this height, you lower control arm angles redirect alot of the force of hitting a bump directly to your 'frame'.
To fix the arm angle, you either have to lower your Jeep

, switch to long arms, or get RE/Trailmaster type drop brackets.
The brackets are probably the cheapest/best way out.
They really do soften up the ride.
The other issue could be your rear lift. Add a Leafs ride pretty stiffly, though at 4.5" alot of the full leaf sets are pretty stiff too.
Running a longer shackle can help the springs ride somewhat softer, but don't expect miracles.
The best bet is to run less arched leafs, with the longer shackles, for the same relative lift.
The only other thing I could think of is if your shocks are too long, or too short (bottoming, or topping out). This can make it ride terribly.
32's & 4.10's is a decent combo. It's a good ratio if you plan to stay at 32". If you have an auto, you
could go with 4.56's if you were planning on going to 33's someday, but I like 4.10's for 32's better myself.
Airing those 32's down a little should help with the ride quality too.
Edit....BTW (about RS9000's) I run RS9009/RS9010 shocks, and they are very soft on their softest two levels, nothing like the rock hard RS5000's